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- PDB-5vg1: Neutron crystallographic structure of a Jonesia denitrificans lyt... -

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Basic information

Entry
Database: PDB / ID: 5vg1
TitleNeutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase
ComponentsChitinase
KeywordsSUGAR BINDING PROTEIN / histidine brace / HYDROLASE
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II ...Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Immunoglobulin E-set / Glycoside hydrolase superfamily
Similarity search - Domain/homology
COPPER (II) ION / PEROXIDE ION / Chitinase
Similarity search - Component
Biological speciesJonesia denitrificans (bacteria)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBacik, J.-P. / Unkefer, C.J. / Chen, J.C.H.
CitationJournal: Biochemistry / Year: 2017
Title: Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.
Authors: Bacik, J.P. / Mekasha, S. / Forsberg, Z. / Kovalevsky, A.Y. / Vaaje-Kolstad, G. / Eijsink, V.G.H. / Nix, J.C. / Coates, L. / Cuneo, M.J. / Unkefer, C.J. / Chen, J.C.
History
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2455
Polymers31,0862
Non-polymers1593
Water4,161231
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6062
Polymers15,5431
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6383
Polymers15,5431
Non-polymers962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.500, 76.400, 122.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase


Mass: 15542.896 Da / Num. of mol.: 2 / Fragment: residues 32-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134) (bacteria)
Strain: ATCC 14870 / DSM 20603 / CIP 55134 / Gene: Jden_1381 / Production host: Escherichia coli (E. coli) / References: UniProt: C7R4I0, chitinase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Purified enzyme was incubated with a threefold molar excess of CuSO4 for 30 min at room temperature. To remove excess copper, the protein was loaded onto a desalting column equilibrated with ...Details: Purified enzyme was incubated with a threefold molar excess of CuSO4 for 30 min at room temperature. To remove excess copper, the protein was loaded onto a desalting column equilibrated with 20 mM Tris-HCl pH 8.0. 14 ul protein solution at 48 mg/ml was mixed with 14 ul reservoir buffer consisting of 1.9 M DL-malic acid pH 7.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: AREA DETECTOR / Date: May 21, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.1→12 Å / Num. obs: 13989 / % possible obs: 76 % / Redundancy: 4.5 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / % possible all: 59.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHENIXphasing
Mantiddata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VG0

5vg0


Resolution: 2.1→12 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2.38 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.265 686 4.9 %
Rwork0.187 --
obs0.191 13989 76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0025222
NEUTRON DIFFRACTIONf_angle_d0.568788
NEUTRON DIFFRACTIONf_dihedral_angle_d11.892390
NEUTRON DIFFRACTIONf_chiral_restr0.04350
NEUTRON DIFFRACTIONf_plane_restr0.0021025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.26120.35181150.26292181NEUTRON DIFFRACTION64
2.2612-2.4870.32271390.23162544NEUTRON DIFFRACTION74
2.487-2.84270.29481360.21042781NEUTRON DIFFRACTION80
2.8427-3.56590.24641510.19262930NEUTRON DIFFRACTION83
3.5659-12.03290.22261450.14542867NEUTRON DIFFRACTION78

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